John Harshman: Bottlenecks and Trans-Species Variation

[swamidass (S. Joshua Swamidass)]

@John_Harshman

Sorry for the late reply, but I was apparently not allowed to speak for 24 hours.

That is the first day limit. I promoted you, so that should not be a problem again.

@John_Harshman

You are missing the fact that I’m referring not to A-group alleles but to B-group alleles. Based solely on topology, there are at least 5 B-group alleles predating the split but only at least 1 A-group allele.

Ah, I see what you are saying. I might have made an error there. I’ll have to go back, and I want to confirm with a colleague that the A and B group alleles are the same locus. If that is the case, I owe you beer next time I’m in northern California.

Still, because these are exon, it remains unclear how much of this is convergent evolution. It is possible that exposure to the same pathogens causes alleles to evolve independently much more recently. There seems to be strong evidence of convergent evolution, and this analysis did not limit itself to neutral mutations.

I agree that a careful analysis of this data could eventually falsify a bottleneck. I also agree that I might have to revise one of my summaries of the literature. It looks like I might have made an error. However, I do not see the published analysis, as they stand as solid and settled evidence against a bottleneck. At some point, someone needs to do some careful work to hash this out. I’m up for doing it too, as long as I have the right collaborators in place to do it really well.

Why Not Clones?

@John_Harshman

Incidentally, why is a single couple the hypothesis of interest? If Eve was created from Adam’s rib, shouldn’t there be a single individual bottleneck? One may presume that the process, most simply, would have involved the slight engineering of Adam’s genome to excise the Y chromosome and duplicate the X.

Turns out to be a straw man to say they are a clone, for two reasons.

1. Buggs, who brought question, made his appoint against the backdrop of common descent, and as a “bottleneck” of a couple.

2. Both AIG and RTB are actively considering a genetic mosaic model, where Adam and Eve each have different genomes in each gamete.

So for the original question #1, Adam and Eve are not homozygous clones. For the other proposals #2, there is a massive loophole that some are trying to take. This is not a panacea, because they have to start specifying details of how many children Adam and Eve have, and I’m not sure the YEC model can work, but perhaps the RTB model can.

Of course, we can use the same methodology to look for TMR2A, though no one seems to care about this. It is a straw man argument, so I’d rather not contribute to confusion by giving it any air time.

Dreaming of Noah

This however, bring us to the elephant in the room:

@John_Harshman

One might also ask whether it’s possible to examine the Flood scenario, in which there was a complicated bottleneck: One Y chromosome, four X chromosomes, three mitochondrial genomes, and a possibility of 10 of each autosome. Come to think of it, an Adam & Eve scenario, of any sort, would also involve different bottlenecks for autosomes, sex chromosomes, and mitochondria.

Exactly. I looked at this partly here, by looking at the TMR10A time…

@Otto

A related question: how about modeling the anthropologically universal flood bottleneck? That would be TMR10A (Noah and his wife + the three wives of their three sons), and even front-loading Adam and Eve with a diversity of stem cells wouldn’t help with this challenge.

@swamidass

The TMR10A Distribution

image.png895x393 39.4 KB

Here it is. It 181,000 years ago. So, this predicts a mutation rate about 45x higher than we directly observe in humans (if the flood was 4,000 years ago). That is really high. If we try and squeeze all the mutation into a window in the past. That means you are looking at >100x mutation rate than ever observed for >1000 years. That just boggles my mind. I’m very open to finding any models that might work, but this totally stumps me. I just do not see what could work.

This ignores the interbreeding between Neanderthals and Sapiens, which is established by independent means. The analysis is a bit complex, but it does seem to solidly rule out most of the current crop of YEC models, which want there to be a bottleneck of 5 with Noah, and can’t really plausibly make them genetic mosaics.

So What Could Work?

However, all they have to do is posit that (1) the flood was not global, just regional, and (2) God made people outside the Garden, and they have a solution. The major organizations are not going to do this for largely political reasons (not based in Scripture or theology), but it is possible some unaffiliated YECs might take that path. It is possible RTB could take this path, or a variation of it, and this would rescue their model.